Analysis of 111/999 NHS calls and 111 online reports
Quentin Leclerc, Emily Nightingale, Samuel Abbott & Thibaut Jombart, for CMMID
Monday 22 June 2020
1 Data preparation
1.1 Outline
Load scripts: loads libraries and useful scripts used in the analyses; all
.Rfiles contained inscriptsat the root of the factory are automatically loadedLoad data: imports datasets, and may contain some ad hoc changes to the data such as specific data cleaning (not used in other reports), new variables used in the analyses, etc.
1.2 Load packages
library(reportfactory)
library(here)
library(rio)
library(tidyverse)
library(incidence)
library(distcrete)
library(epitrix)
library(earlyR)
library(projections)
library(linelist)
library(remotes)
library(janitor)
library(kableExtra)
library(DT)
library(cyphr)
library(chngpt)
library(lubridate)
library(ggpubr)
library(ggnewscale)1.3 Load scripts
These scripts will load:
- all scripts stored as
.Rfiles inside/scripts/ - all scripts stored as
.Rfiles inside/src/
These scripts also contain routines to access the latest clean encrypted data (see next section).
1.4 Load clean data
We import the latest NHS pathways data:
x <- import_pathways() %>%
as_tibble()
x
## [90m# A tibble: 153,678 x 11[39m
## site_type date sex age ccg_code ccg_name count postcode nhs_region
## [3m[90m<chr>[39m[23m [3m[90m<date>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<int>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<chr>[39m[23m
## [90m 1[39m 111 2020-03-18 fema… 0-18 e380000… nhs_bar… 35 rm13ae London
## [90m 2[39m 111 2020-03-18 fema… 0-18 e380000… nhs_bed… 27 mk454hr East of E…
## [90m 3[39m 111 2020-03-18 fema… 0-18 e380000… nhs_bla… 9 bb12fd North West
## [90m 4[39m 111 2020-03-18 fema… 0-18 e380000… nhs_bro… 11 br33ql London
## [90m 5[39m 111 2020-03-18 fema… 0-18 e380000… nhs_can… 9 ws111jp Midlands
## [90m 6[39m 111 2020-03-18 fema… 0-18 e380000… nhs_cit… 12 n15lz London
## [90m 7[39m 111 2020-03-18 fema… 0-18 e380000… nhs_enf… 7 en40dy London
## [90m 8[39m 111 2020-03-18 fema… 0-18 e380000… nhs_ham… 6 dl62uu North Eas…
## [90m 9[39m 111 2020-03-18 fema… 0-18 e380000… nhs_har… 24 ts232la North Eas…
## [90m10[39m 111 2020-03-18 fema… 0-18 e380000… nhs_kin… 6 kt11eu London
## [90m# … with 153,668 more rows, and 2 more variables: day [3m[90m<int>[90m[23m, weekday [3m[90m<fct>[90m[23m[39mWe also import demographics data for NHS regions in England, used later in our analysis:
path <- here::here("data", "csv", "nhs_region_population_2018.csv")
nhs_region_pop <- rio::import(path) %>%
mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))
nhs_region_pop$nhs_region <- gsub(" Of ", " of ", nhs_region_pop$nhs_region)
nhs_region_pop$nhs_region <- gsub(" And ", " and ", nhs_region_pop$nhs_region)
nhs_region_pop
## nhs_region variable value
## 1 North West 0-18 0.22538599
## 2 North East and Yorkshire 0-18 0.21876449
## 3 Midlands 0-18 0.22564656
## 4 East of England 0-18 0.22810783
## 5 London 0-18 0.23764782
## 6 South East 0-18 0.22458811
## 7 South West 0-18 0.20799797
## 8 North West 19-69 0.64274078
## 9 North East and Yorkshire 19-69 0.64437753
## 10 Midlands 19-69 0.63876675
## 11 East of England 19-69 0.63034229
## 12 London 19-69 0.67820084
## 13 South East 19-69 0.63267336
## 14 South West 19-69 0.63176131
## 15 North West 70-120 0.13187323
## 16 North East and Yorkshire 70-120 0.13685797
## 17 Midlands 70-120 0.13558669
## 18 East of England 70-120 0.14154988
## 19 London 70-120 0.08415135
## 20 South East 70-120 0.14273853
## 21 South West 70-120 0.16024072Finally, we import publically available deaths per NHS region:
dth <- import_deaths() %>%
mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))
#truncation to account for reporting delay
delay_max <- 21
dth$nhs_region <- gsub(" Of ", " of ", dth$nhs_region)
dth$nhs_region <- gsub(" And ", " and ", dth$nhs_region)
dth
## date_report nhs_region deaths
## 1 2020-03-01 East of England 0
## 2 2020-03-02 East of England 1
## 3 2020-03-03 East of England 0
## 4 2020-03-04 East of England 0
## 5 2020-03-05 East of England 0
## 6 2020-03-06 East of England 1
## 7 2020-03-07 East of England 0
## 8 2020-03-08 East of England 0
## 9 2020-03-09 East of England 1
## 10 2020-03-10 East of England 0
## 11 2020-03-11 East of England 0
## 12 2020-03-12 East of England 0
## 13 2020-03-13 East of England 1
## 14 2020-03-14 East of England 2
## 15 2020-03-15 East of England 2
## 16 2020-03-16 East of England 1
## 17 2020-03-17 East of England 1
## 18 2020-03-18 East of England 5
## 19 2020-03-19 East of England 4
## 20 2020-03-20 East of England 2
## 21 2020-03-21 East of England 11
## 22 2020-03-22 East of England 12
## 23 2020-03-23 East of England 11
## 24 2020-03-24 East of England 19
## 25 2020-03-25 East of England 26
## 26 2020-03-26 East of England 36
## 27 2020-03-27 East of England 38
## 28 2020-03-28 East of England 28
## 29 2020-03-29 East of England 43
## 30 2020-03-30 East of England 45
## 31 2020-03-31 East of England 70
## 32 2020-04-01 East of England 62
## 33 2020-04-02 East of England 64
## 34 2020-04-03 East of England 80
## 35 2020-04-04 East of England 71
## 36 2020-04-05 East of England 76
## 37 2020-04-06 East of England 71
## 38 2020-04-07 East of England 93
## 39 2020-04-08 East of England 111
## 40 2020-04-09 East of England 87
## 41 2020-04-10 East of England 74
## 42 2020-04-11 East of England 92
## 43 2020-04-12 East of England 101
## 44 2020-04-13 East of England 78
## 45 2020-04-14 East of England 61
## 46 2020-04-15 East of England 82
## 47 2020-04-16 East of England 74
## 48 2020-04-17 East of England 86
## 49 2020-04-18 East of England 64
## 50 2020-04-19 East of England 67
## 51 2020-04-20 East of England 67
## 52 2020-04-21 East of England 75
## 53 2020-04-22 East of England 67
## 54 2020-04-23 East of England 49
## 55 2020-04-24 East of England 66
## 56 2020-04-25 East of England 54
## 57 2020-04-26 East of England 48
## 58 2020-04-27 East of England 46
## 59 2020-04-28 East of England 58
## 60 2020-04-29 East of England 32
## 61 2020-04-30 East of England 45
## 62 2020-05-01 East of England 49
## 63 2020-05-02 East of England 29
## 64 2020-05-03 East of England 41
## 65 2020-05-04 East of England 19
## 66 2020-05-05 East of England 36
## 67 2020-05-06 East of England 31
## 68 2020-05-07 East of England 33
## 69 2020-05-08 East of England 33
## 70 2020-05-09 East of England 29
## 71 2020-05-10 East of England 22
## 72 2020-05-11 East of England 18
## 73 2020-05-12 East of England 21
## 74 2020-05-13 East of England 27
## 75 2020-05-14 East of England 26
## 76 2020-05-15 East of England 19
## 77 2020-05-16 East of England 26
## 78 2020-05-17 East of England 17
## 79 2020-05-18 East of England 25
## 80 2020-05-19 East of England 15
## 81 2020-05-20 East of England 26
## 82 2020-05-21 East of England 21
## 83 2020-05-22 East of England 13
## 84 2020-05-23 East of England 12
## 85 2020-05-24 East of England 17
## 86 2020-05-25 East of England 25
## 87 2020-05-26 East of England 14
## 88 2020-05-27 East of England 12
## 89 2020-05-28 East of England 17
## 90 2020-05-29 East of England 16
## 91 2020-05-30 East of England 9
## 92 2020-05-31 East of England 8
## 93 2020-06-01 East of England 17
## 94 2020-06-02 East of England 14
## 95 2020-06-03 East of England 10
## 96 2020-06-04 East of England 7
## 97 2020-06-05 East of England 12
## 98 2020-06-06 East of England 5
## 99 2020-06-07 East of England 9
## 100 2020-06-08 East of England 5
## 101 2020-06-09 East of England 6
## 102 2020-06-10 East of England 8
## 103 2020-06-11 East of England 0
## 104 2020-06-12 East of England 9
## 105 2020-06-13 East of England 5
## 106 2020-06-14 East of England 4
## 107 2020-06-15 East of England 7
## 108 2020-06-16 East of England 3
## 109 2020-06-17 East of England 7
## 110 2020-06-18 East of England 3
## 111 2020-06-19 East of England 5
## 112 2020-06-20 East of England 0
## 113 2020-03-01 London 0
## 114 2020-03-02 London 0
## 115 2020-03-03 London 0
## 116 2020-03-04 London 0
## 117 2020-03-05 London 0
## 118 2020-03-06 London 1
## 119 2020-03-07 London 0
## 120 2020-03-08 London 0
## 121 2020-03-09 London 1
## 122 2020-03-10 London 0
## 123 2020-03-11 London 6
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## 125 2020-03-13 London 10
## 126 2020-03-14 London 14
## 127 2020-03-15 London 10
## 128 2020-03-16 London 15
## 129 2020-03-17 London 23
## 130 2020-03-18 London 27
## 131 2020-03-19 London 25
## 132 2020-03-20 London 44
## 133 2020-03-21 London 49
## 134 2020-03-22 London 54
## 135 2020-03-23 London 63
## 136 2020-03-24 London 87
## 137 2020-03-25 London 113
## 138 2020-03-26 London 129
## 139 2020-03-27 London 130
## 140 2020-03-28 London 122
## 141 2020-03-29 London 146
## 142 2020-03-30 London 149
## 143 2020-03-31 London 181
## 144 2020-04-01 London 202
## 145 2020-04-02 London 190
## 146 2020-04-03 London 196
## 147 2020-04-04 London 230
## 148 2020-04-05 London 195
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## 151 2020-04-08 London 238
## 152 2020-04-09 London 206
## 153 2020-04-10 London 170
## 154 2020-04-11 London 178
## 155 2020-04-12 London 158
## 156 2020-04-13 London 166
## 157 2020-04-14 London 144
## 158 2020-04-15 London 142
## 159 2020-04-16 London 139
## 160 2020-04-17 London 100
## 161 2020-04-18 London 101
## 162 2020-04-19 London 103
## 163 2020-04-20 London 95
## 164 2020-04-21 London 94
## 165 2020-04-22 London 109
## 166 2020-04-23 London 77
## 167 2020-04-24 London 71
## 168 2020-04-25 London 58
## 169 2020-04-26 London 53
## 170 2020-04-27 London 51
## 171 2020-04-28 London 43
## 172 2020-04-29 London 44
## 173 2020-04-30 London 40
## 174 2020-05-01 London 41
## 175 2020-05-02 London 41
## 176 2020-05-03 London 36
## 177 2020-05-04 London 30
## 178 2020-05-05 London 25
## 179 2020-05-06 London 37
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## 190 2020-05-17 London 15
## 191 2020-05-18 London 9
## 192 2020-05-19 London 14
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## 194 2020-05-21 London 12
## 195 2020-05-22 London 10
## 196 2020-05-23 London 6
## 197 2020-05-24 London 7
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## 200 2020-05-27 London 7
## 201 2020-05-28 London 8
## 202 2020-05-29 London 7
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## 206 2020-06-02 London 7
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## 210 2020-06-06 London 0
## 211 2020-06-07 London 4
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## 213 2020-06-09 London 4
## 214 2020-06-10 London 7
## 215 2020-06-11 London 5
## 216 2020-06-12 London 3
## 217 2020-06-13 London 3
## 218 2020-06-14 London 2
## 219 2020-06-15 London 1
## 220 2020-06-16 London 2
## 221 2020-06-17 London 1
## 222 2020-06-18 London 2
## 223 2020-06-19 London 0
## 224 2020-06-20 London 0
## 225 2020-03-01 Midlands 0
## 226 2020-03-02 Midlands 0
## 227 2020-03-03 Midlands 1
## 228 2020-03-04 Midlands 0
## 229 2020-03-05 Midlands 0
## 230 2020-03-06 Midlands 0
## 231 2020-03-07 Midlands 0
## 232 2020-03-08 Midlands 3
## 233 2020-03-09 Midlands 1
## 234 2020-03-10 Midlands 0
## 235 2020-03-11 Midlands 2
## 236 2020-03-12 Midlands 6
## 237 2020-03-13 Midlands 5
## 238 2020-03-14 Midlands 4
## 239 2020-03-15 Midlands 5
## 240 2020-03-16 Midlands 11
## 241 2020-03-17 Midlands 8
## 242 2020-03-18 Midlands 13
## 243 2020-03-19 Midlands 8
## 244 2020-03-20 Midlands 28
## 245 2020-03-21 Midlands 13
## 246 2020-03-22 Midlands 31
## 247 2020-03-23 Midlands 33
## 248 2020-03-24 Midlands 41
## 249 2020-03-25 Midlands 48
## 250 2020-03-26 Midlands 64
## 251 2020-03-27 Midlands 72
## 252 2020-03-28 Midlands 89
## 253 2020-03-29 Midlands 92
## 254 2020-03-30 Midlands 90
## 255 2020-03-31 Midlands 123
## 256 2020-04-01 Midlands 140
## 257 2020-04-02 Midlands 142
## 258 2020-04-03 Midlands 124
## 259 2020-04-04 Midlands 151
## 260 2020-04-05 Midlands 164
## 261 2020-04-06 Midlands 140
## 262 2020-04-07 Midlands 123
## 263 2020-04-08 Midlands 186
## 264 2020-04-09 Midlands 139
## 265 2020-04-10 Midlands 127
## 266 2020-04-11 Midlands 142
## 267 2020-04-12 Midlands 139
## 268 2020-04-13 Midlands 120
## 269 2020-04-14 Midlands 116
## 270 2020-04-15 Midlands 147
## 271 2020-04-16 Midlands 102
## 272 2020-04-17 Midlands 118
## 273 2020-04-18 Midlands 115
## 274 2020-04-19 Midlands 92
## 275 2020-04-20 Midlands 107
## 276 2020-04-21 Midlands 86
## 277 2020-04-22 Midlands 78
## 278 2020-04-23 Midlands 103
## 279 2020-04-24 Midlands 79
## 280 2020-04-25 Midlands 72
## 281 2020-04-26 Midlands 81
## 282 2020-04-27 Midlands 74
## 283 2020-04-28 Midlands 68
## 284 2020-04-29 Midlands 53
## 285 2020-04-30 Midlands 56
## 286 2020-05-01 Midlands 64
## 287 2020-05-02 Midlands 51
## 288 2020-05-03 Midlands 52
## 289 2020-05-04 Midlands 61
## 290 2020-05-05 Midlands 58
## 291 2020-05-06 Midlands 59
## 292 2020-05-07 Midlands 48
## 293 2020-05-08 Midlands 34
## 294 2020-05-09 Midlands 37
## 295 2020-05-10 Midlands 42
## 296 2020-05-11 Midlands 33
## 297 2020-05-12 Midlands 45
## 298 2020-05-13 Midlands 40
## 299 2020-05-14 Midlands 37
## 300 2020-05-15 Midlands 40
## 301 2020-05-16 Midlands 34
## 302 2020-05-17 Midlands 31
## 303 2020-05-18 Midlands 34
## 304 2020-05-19 Midlands 34
## 305 2020-05-20 Midlands 36
## 306 2020-05-21 Midlands 32
## 307 2020-05-22 Midlands 27
## 308 2020-05-23 Midlands 34
## 309 2020-05-24 Midlands 19
## 310 2020-05-25 Midlands 26
## 311 2020-05-26 Midlands 33
## 312 2020-05-27 Midlands 29
## 313 2020-05-28 Midlands 27
## 314 2020-05-29 Midlands 20
## 315 2020-05-30 Midlands 20
## 316 2020-05-31 Midlands 22
## 317 2020-06-01 Midlands 20
## 318 2020-06-02 Midlands 22
## 319 2020-06-03 Midlands 24
## 320 2020-06-04 Midlands 15
## 321 2020-06-05 Midlands 21
## 322 2020-06-06 Midlands 20
## 323 2020-06-07 Midlands 16
## 324 2020-06-08 Midlands 15
## 325 2020-06-09 Midlands 17
## 326 2020-06-10 Midlands 15
## 327 2020-06-11 Midlands 13
## 328 2020-06-12 Midlands 12
## 329 2020-06-13 Midlands 6
## 330 2020-06-14 Midlands 17
## 331 2020-06-15 Midlands 12
## 332 2020-06-16 Midlands 13
## 333 2020-06-17 Midlands 10
## 334 2020-06-18 Midlands 14
## 335 2020-06-19 Midlands 6
## 336 2020-06-20 Midlands 2
## 337 2020-03-01 North East and Yorkshire 0
## 338 2020-03-02 North East and Yorkshire 0
## 339 2020-03-03 North East and Yorkshire 0
## 340 2020-03-04 North East and Yorkshire 0
## 341 2020-03-05 North East and Yorkshire 0
## 342 2020-03-06 North East and Yorkshire 0
## 343 2020-03-07 North East and Yorkshire 0
## 344 2020-03-08 North East and Yorkshire 0
## 345 2020-03-09 North East and Yorkshire 0
## 346 2020-03-10 North East and Yorkshire 0
## 347 2020-03-11 North East and Yorkshire 0
## 348 2020-03-12 North East and Yorkshire 0
## 349 2020-03-13 North East and Yorkshire 0
## 350 2020-03-14 North East and Yorkshire 0
## 351 2020-03-15 North East and Yorkshire 2
## 352 2020-03-16 North East and Yorkshire 3
## 353 2020-03-17 North East and Yorkshire 1
## 354 2020-03-18 North East and Yorkshire 2
## 355 2020-03-19 North East and Yorkshire 6
## 356 2020-03-20 North East and Yorkshire 5
## 357 2020-03-21 North East and Yorkshire 6
## 358 2020-03-22 North East and Yorkshire 7
## 359 2020-03-23 North East and Yorkshire 9
## 360 2020-03-24 North East and Yorkshire 8
## 361 2020-03-25 North East and Yorkshire 18
## 362 2020-03-26 North East and Yorkshire 21
## 363 2020-03-27 North East and Yorkshire 28
## 364 2020-03-28 North East and Yorkshire 35
## 365 2020-03-29 North East and Yorkshire 38
## 366 2020-03-30 North East and Yorkshire 64
## 367 2020-03-31 North East and Yorkshire 60
## 368 2020-04-01 North East and Yorkshire 67
## 369 2020-04-02 North East and Yorkshire 74
## 370 2020-04-03 North East and Yorkshire 100
## 371 2020-04-04 North East and Yorkshire 105
## 372 2020-04-05 North East and Yorkshire 92
## 373 2020-04-06 North East and Yorkshire 96
## 374 2020-04-07 North East and Yorkshire 102
## 375 2020-04-08 North East and Yorkshire 107
## 376 2020-04-09 North East and Yorkshire 111
## 377 2020-04-10 North East and Yorkshire 117
## 378 2020-04-11 North East and Yorkshire 98
## 379 2020-04-12 North East and Yorkshire 84
## 380 2020-04-13 North East and Yorkshire 94
## 381 2020-04-14 North East and Yorkshire 107
## 382 2020-04-15 North East and Yorkshire 96
## 383 2020-04-16 North East and Yorkshire 103
## 384 2020-04-17 North East and Yorkshire 88
## 385 2020-04-18 North East and Yorkshire 95
## 386 2020-04-19 North East and Yorkshire 88
## 387 2020-04-20 North East and Yorkshire 100
## 388 2020-04-21 North East and Yorkshire 76
## 389 2020-04-22 North East and Yorkshire 84
## 390 2020-04-23 North East and Yorkshire 63
## 391 2020-04-24 North East and Yorkshire 72
## 392 2020-04-25 North East and Yorkshire 69
## 393 2020-04-26 North East and Yorkshire 65
## 394 2020-04-27 North East and Yorkshire 65
## 395 2020-04-28 North East and Yorkshire 57
## 396 2020-04-29 North East and Yorkshire 69
## 397 2020-04-30 North East and Yorkshire 57
## 398 2020-05-01 North East and Yorkshire 64
## 399 2020-05-02 North East and Yorkshire 48
## 400 2020-05-03 North East and Yorkshire 40
## 401 2020-05-04 North East and Yorkshire 49
## 402 2020-05-05 North East and Yorkshire 40
## 403 2020-05-06 North East and Yorkshire 51
## 404 2020-05-07 North East and Yorkshire 45
## 405 2020-05-08 North East and Yorkshire 42
## 406 2020-05-09 North East and Yorkshire 44
## 407 2020-05-10 North East and Yorkshire 40
## 408 2020-05-11 North East and Yorkshire 29
## 409 2020-05-12 North East and Yorkshire 27
## 410 2020-05-13 North East and Yorkshire 28
## 411 2020-05-14 North East and Yorkshire 30
## 412 2020-05-15 North East and Yorkshire 32
## 413 2020-05-16 North East and Yorkshire 35
## 414 2020-05-17 North East and Yorkshire 26
## 415 2020-05-18 North East and Yorkshire 29
## 416 2020-05-19 North East and Yorkshire 27
## 417 2020-05-20 North East and Yorkshire 21
## 418 2020-05-21 North East and Yorkshire 33
## 419 2020-05-22 North East and Yorkshire 22
## 420 2020-05-23 North East and Yorkshire 18
## 421 2020-05-24 North East and Yorkshire 25
## 422 2020-05-25 North East and Yorkshire 21
## 423 2020-05-26 North East and Yorkshire 21
## 424 2020-05-27 North East and Yorkshire 22
## 425 2020-05-28 North East and Yorkshire 20
## 426 2020-05-29 North East and Yorkshire 25
## 427 2020-05-30 North East and Yorkshire 20
## 428 2020-05-31 North East and Yorkshire 20
## 429 2020-06-01 North East and Yorkshire 16
## 430 2020-06-02 North East and Yorkshire 22
## 431 2020-06-03 North East and Yorkshire 22
## 432 2020-06-04 North East and Yorkshire 17
## 433 2020-06-05 North East and Yorkshire 17
## 434 2020-06-06 North East and Yorkshire 21
## 435 2020-06-07 North East and Yorkshire 13
## 436 2020-06-08 North East and Yorkshire 11
## 437 2020-06-09 North East and Yorkshire 11
## 438 2020-06-10 North East and Yorkshire 18
## 439 2020-06-11 North East and Yorkshire 7
## 440 2020-06-12 North East and Yorkshire 9
## 441 2020-06-13 North East and Yorkshire 10
## 442 2020-06-14 North East and Yorkshire 11
## 443 2020-06-15 North East and Yorkshire 8
## 444 2020-06-16 North East and Yorkshire 10
## 445 2020-06-17 North East and Yorkshire 6
## 446 2020-06-18 North East and Yorkshire 7
## 447 2020-06-19 North East and Yorkshire 2
## 448 2020-06-20 North East and Yorkshire 3
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## 461 2020-03-13 North West 3
## 462 2020-03-14 North West 1
## 463 2020-03-15 North West 4
## 464 2020-03-16 North West 2
## 465 2020-03-17 North West 4
## 466 2020-03-18 North West 6
## 467 2020-03-19 North West 7
## 468 2020-03-20 North West 10
## 469 2020-03-21 North West 11
## 470 2020-03-22 North West 13
## 471 2020-03-23 North West 15
## 472 2020-03-24 North West 21
## 473 2020-03-25 North West 21
## 474 2020-03-26 North West 29
## 475 2020-03-27 North West 35
## 476 2020-03-28 North West 28
## 477 2020-03-29 North West 46
## 478 2020-03-30 North West 67
## 479 2020-03-31 North West 52
## 480 2020-04-01 North West 86
## 481 2020-04-02 North West 96
## 482 2020-04-03 North West 95
## 483 2020-04-04 North West 98
## 484 2020-04-05 North West 102
## 485 2020-04-06 North West 100
## 486 2020-04-07 North West 135
## 487 2020-04-08 North West 127
## 488 2020-04-09 North West 119
## 489 2020-04-10 North West 117
## 490 2020-04-11 North West 138
## 491 2020-04-12 North West 125
## 492 2020-04-13 North West 129
## 493 2020-04-14 North West 131
## 494 2020-04-15 North West 114
## 495 2020-04-16 North West 135
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## 501 2020-04-22 North West 86
## 502 2020-04-23 North West 85
## 503 2020-04-24 North West 66
## 504 2020-04-25 North West 65
## 505 2020-04-26 North West 55
## 506 2020-04-27 North West 54
## 507 2020-04-28 North West 57
## 508 2020-04-29 North West 62
## 509 2020-04-30 North West 59
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## 511 2020-05-02 North West 56
## 512 2020-05-03 North West 55
## 513 2020-05-04 North West 48
## 514 2020-05-05 North West 48
## 515 2020-05-06 North West 44
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## 518 2020-05-09 North West 30
## 519 2020-05-10 North West 41
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## 521 2020-05-12 North West 38
## 522 2020-05-13 North West 25
## 523 2020-05-14 North West 26
## 524 2020-05-15 North West 33
## 525 2020-05-16 North West 32
## 526 2020-05-17 North West 24
## 527 2020-05-18 North West 31
## 528 2020-05-19 North West 35
## 529 2020-05-20 North West 27
## 530 2020-05-21 North West 26
## 531 2020-05-22 North West 26
## 532 2020-05-23 North West 31
## 533 2020-05-24 North West 26
## 534 2020-05-25 North West 31
## 535 2020-05-26 North West 27
## 536 2020-05-27 North West 27
## 537 2020-05-28 North West 28
## 538 2020-05-29 North West 20
## 539 2020-05-30 North West 19
## 540 2020-05-31 North West 13
## 541 2020-06-01 North West 12
## 542 2020-06-02 North West 27
## 543 2020-06-03 North West 22
## 544 2020-06-04 North West 22
## 545 2020-06-05 North West 15
## 546 2020-06-06 North West 23
## 547 2020-06-07 North West 19
## 548 2020-06-08 North West 20
## 549 2020-06-09 North West 15
## 550 2020-06-10 North West 14
## 551 2020-06-11 North West 16
## 552 2020-06-12 North West 7
## 553 2020-06-13 North West 8
## 554 2020-06-14 North West 15
## 555 2020-06-15 North West 14
## 556 2020-06-16 North West 11
## 557 2020-06-17 North West 10
## 558 2020-06-18 North West 6
## 559 2020-06-19 North West 5
## 560 2020-06-20 North West 1
## 561 2020-03-01 South East 0
## 562 2020-03-02 South East 0
## 563 2020-03-03 South East 1
## 564 2020-03-04 South East 0
## 565 2020-03-05 South East 1
## 566 2020-03-06 South East 0
## 567 2020-03-07 South East 0
## 568 2020-03-08 South East 1
## 569 2020-03-09 South East 1
## 570 2020-03-10 South East 1
## 571 2020-03-11 South East 1
## 572 2020-03-12 South East 0
## 573 2020-03-13 South East 1
## 574 2020-03-14 South East 1
## 575 2020-03-15 South East 5
## 576 2020-03-16 South East 8
## 577 2020-03-17 South East 7
## 578 2020-03-18 South East 10
## 579 2020-03-19 South East 9
## 580 2020-03-20 South East 13
## 581 2020-03-21 South East 7
## 582 2020-03-22 South East 25
## 583 2020-03-23 South East 20
## 584 2020-03-24 South East 22
## 585 2020-03-25 South East 29
## 586 2020-03-26 South East 35
## 587 2020-03-27 South East 34
## 588 2020-03-28 South East 36
## 589 2020-03-29 South East 55
## 590 2020-03-30 South East 58
## 591 2020-03-31 South East 65
## 592 2020-04-01 South East 66
## 593 2020-04-02 South East 55
## 594 2020-04-03 South East 72
## 595 2020-04-04 South East 80
## 596 2020-04-05 South East 82
## 597 2020-04-06 South East 88
## 598 2020-04-07 South East 100
## 599 2020-04-08 South East 83
## 600 2020-04-09 South East 104
## 601 2020-04-10 South East 88
## 602 2020-04-11 South East 88
## 603 2020-04-12 South East 88
## 604 2020-04-13 South East 84
## 605 2020-04-14 South East 65
## 606 2020-04-15 South East 72
## 607 2020-04-16 South East 56
## 608 2020-04-17 South East 86
## 609 2020-04-18 South East 57
## 610 2020-04-19 South East 70
## 611 2020-04-20 South East 87
## 612 2020-04-21 South East 50
## 613 2020-04-22 South East 54
## 614 2020-04-23 South East 57
## 615 2020-04-24 South East 64
## 616 2020-04-25 South East 51
## 617 2020-04-26 South East 51
## 618 2020-04-27 South East 40
## 619 2020-04-28 South East 40
## 620 2020-04-29 South East 47
## 621 2020-04-30 South East 29
## 622 2020-05-01 South East 37
## 623 2020-05-02 South East 36
## 624 2020-05-03 South East 17
## 625 2020-05-04 South East 35
## 626 2020-05-05 South East 29
## 627 2020-05-06 South East 25
## 628 2020-05-07 South East 27
## 629 2020-05-08 South East 26
## 630 2020-05-09 South East 28
## 631 2020-05-10 South East 19
## 632 2020-05-11 South East 25
## 633 2020-05-12 South East 27
## 634 2020-05-13 South East 18
## 635 2020-05-14 South East 32
## 636 2020-05-15 South East 24
## 637 2020-05-16 South East 22
## 638 2020-05-17 South East 18
## 639 2020-05-18 South East 22
## 640 2020-05-19 South East 12
## 641 2020-05-20 South East 22
## 642 2020-05-21 South East 15
## 643 2020-05-22 South East 17
## 644 2020-05-23 South East 21
## 645 2020-05-24 South East 17
## 646 2020-05-25 South East 13
## 647 2020-05-26 South East 19
## 648 2020-05-27 South East 18
## 649 2020-05-28 South East 12
## 650 2020-05-29 South East 21
## 651 2020-05-30 South East 8
## 652 2020-05-31 South East 10
## 653 2020-06-01 South East 11
## 654 2020-06-02 South East 13
## 655 2020-06-03 South East 17
## 656 2020-06-04 South East 11
## 657 2020-06-05 South East 11
## 658 2020-06-06 South East 10
## 659 2020-06-07 South East 11
## 660 2020-06-08 South East 7
## 661 2020-06-09 South East 10
## 662 2020-06-10 South East 10
## 663 2020-06-11 South East 5
## 664 2020-06-12 South East 5
## 665 2020-06-13 South East 4
## 666 2020-06-14 South East 6
## 667 2020-06-15 South East 7
## 668 2020-06-16 South East 10
## 669 2020-06-17 South East 8
## 670 2020-06-18 South East 4
## 671 2020-06-19 South East 4
## 672 2020-06-20 South East 0
## 673 2020-03-01 South West 0
## 674 2020-03-02 South West 0
## 675 2020-03-03 South West 0
## 676 2020-03-04 South West 0
## 677 2020-03-05 South West 0
## 678 2020-03-06 South West 0
## 679 2020-03-07 South West 0
## 680 2020-03-08 South West 0
## 681 2020-03-09 South West 0
## 682 2020-03-10 South West 0
## 683 2020-03-11 South West 1
## 684 2020-03-12 South West 0
## 685 2020-03-13 South West 0
## 686 2020-03-14 South West 1
## 687 2020-03-15 South West 0
## 688 2020-03-16 South West 0
## 689 2020-03-17 South West 2
## 690 2020-03-18 South West 2
## 691 2020-03-19 South West 4
## 692 2020-03-20 South West 3
## 693 2020-03-21 South West 6
## 694 2020-03-22 South West 7
## 695 2020-03-23 South West 8
## 696 2020-03-24 South West 7
## 697 2020-03-25 South West 9
## 698 2020-03-26 South West 11
## 699 2020-03-27 South West 13
## 700 2020-03-28 South West 21
## 701 2020-03-29 South West 18
## 702 2020-03-30 South West 23
## 703 2020-03-31 South West 23
## 704 2020-04-01 South West 22
## 705 2020-04-02 South West 23
## 706 2020-04-03 South West 30
## 707 2020-04-04 South West 42
## 708 2020-04-05 South West 32
## 709 2020-04-06 South West 34
## 710 2020-04-07 South West 39
## 711 2020-04-08 South West 47
## 712 2020-04-09 South West 24
## 713 2020-04-10 South West 46
## 714 2020-04-11 South West 43
## 715 2020-04-12 South West 23
## 716 2020-04-13 South West 27
## 717 2020-04-14 South West 24
## 718 2020-04-15 South West 32
## 719 2020-04-16 South West 29
## 720 2020-04-17 South West 33
## 721 2020-04-18 South West 25
## 722 2020-04-19 South West 31
## 723 2020-04-20 South West 26
## 724 2020-04-21 South West 26
## 725 2020-04-22 South West 23
## 726 2020-04-23 South West 17
## 727 2020-04-24 South West 19
## 728 2020-04-25 South West 15
## 729 2020-04-26 South West 27
## 730 2020-04-27 South West 13
## 731 2020-04-28 South West 17
## 732 2020-04-29 South West 15
## 733 2020-04-30 South West 26
## 734 2020-05-01 South West 6
## 735 2020-05-02 South West 7
## 736 2020-05-03 South West 10
## 737 2020-05-04 South West 17
## 738 2020-05-05 South West 14
## 739 2020-05-06 South West 19
## 740 2020-05-07 South West 16
## 741 2020-05-08 South West 6
## 742 2020-05-09 South West 11
## 743 2020-05-10 South West 5
## 744 2020-05-11 South West 8
## 745 2020-05-12 South West 7
## 746 2020-05-13 South West 7
## 747 2020-05-14 South West 6
## 748 2020-05-15 South West 4
## 749 2020-05-16 South West 4
## 750 2020-05-17 South West 6
## 751 2020-05-18 South West 4
## 752 2020-05-19 South West 6
## 753 2020-05-20 South West 1
## 754 2020-05-21 South West 9
## 755 2020-05-22 South West 6
## 756 2020-05-23 South West 6
## 757 2020-05-24 South West 3
## 758 2020-05-25 South West 8
## 759 2020-05-26 South West 11
## 760 2020-05-27 South West 5
## 761 2020-05-28 South West 10
## 762 2020-05-29 South West 7
## 763 2020-05-30 South West 3
## 764 2020-05-31 South West 2
## 765 2020-06-01 South West 7
## 766 2020-06-02 South West 2
## 767 2020-06-03 South West 5
## 768 2020-06-04 South West 2
## 769 2020-06-05 South West 2
## 770 2020-06-06 South West 1
## 771 2020-06-07 South West 3
## 772 2020-06-08 South West 3
## 773 2020-06-09 South West 0
## 774 2020-06-10 South West 0
## 775 2020-06-11 South West 2
## 776 2020-06-12 South West 2
## 777 2020-06-13 South West 2
## 778 2020-06-14 South West 0
## 779 2020-06-15 South West 1
## 780 2020-06-16 South West 1
## 781 2020-06-17 South West 0
## 782 2020-06-18 South West 0
## 783 2020-06-19 South West 0
## 784 2020-06-20 South West 11.5 Completion date
We extract the completion date from the NHS Pathways file timestamp:
The completion date of the NHS Pathways data is Sunday 21 Jun 2020.
1.6 Auxiliary functions
These are functions which will be used further in the analyses.
Function to estimate the generalised R-squared as the proportion of deviance explained by a given model:
## Function to calculate R2 for Poisson model
## not adjusted for model complexity but all models have the same DF here
Rsq <- function(x) {
1 - (x$deviance / x$null.deviance)
}Function to extract growth rates per region as well as halving times, and the associated 95% confidence intervals:
## function to extract the coefficients, find the level of the intercept,
## reconstruct the values of r, get confidence intervals
get_r <- function(model) {
## extract coefficients and conf int
out <- data.frame(r = coef(model)) %>%
rownames_to_column("var") %>%
cbind(confint(model)) %>%
filter(!grepl("day_of_week", var)) %>%
filter(grepl("day", var)) %>%
rename(lower_95 = "2.5 %",
upper_95 = "97.5 %") %>%
mutate(var = sub("day:", "", var))
## reconstruct values: intercept + region-coefficient
for (i in 2:nrow(out)) {
out[i, -1] <- out[1, -1] + out[i, -1]
}
## find the name of the intercept, restore regions names
out <- out %>%
mutate(nhs_region = model$xlevels$nhs_region) %>%
select(nhs_region, everything(), -var)
## find halving times
halving <- log(0.5) / out[,-1] %>%
rename(halving_t = r,
halving_t_lower_95 = lower_95,
halving_t_upper_95 = upper_95)
## set halving times with exclusion intervals to NA
no_halving <- out$lower_95 < 0 & out$upper_95 > 0
halving[no_halving, ] <- NA_real_
## return all data
cbind(out, halving)
}Functions used in the correlation analysis between NHS Pathways reports and deaths:
## Function to calculate Pearson's correlation between deaths and lagged
## reports. Note that `pearson` can be replaced with `spearman` for rank
## correlation.
getcor <- function(x, ndx) {
return(cor(x$deaths[ndx],
x$note_lag[ndx],
use = "complete.obs",
method = "pearson"))
}
## Catch if sample size throws an error
getcor2 <- possibly(getcor, otherwise = NA)
getboot <- function(x) {
result <- boot::boot.ci(boot::boot(x, getcor2, R = 1000),
type = "bca")
return(data.frame(n = sum(!is.na(x$note_lag) & !is.na(x$deaths)),
r = result$t0,
r_low = result$bca[4],
r_hi = result$bca[5]))
}Function to classify the day of the week into weekend, Monday, and the rest:
## Fn to add day of week
day_of_week <- function(df) {
df %>%
dplyr::mutate(day_of_week = lubridate::wday(date, label = TRUE)) %>%
dplyr::mutate(day_of_week = dplyr::case_when(
day_of_week %in% c("Sat", "Sun") ~ "weekend",
day_of_week %in% c("Mon") ~ "monday",
!(day_of_week %in% c("Sat", "Sun", "Mon")) ~ "rest_of_week"
) %>%
factor(levels = c("rest_of_week", "monday", "weekend")))
}Custom color palettes, color scales, and vectors of colors:
2 Temporal trends in NHS Pathways reports
2.1 Outline
We look for temporal patterns in COVID-19 related 111/999 calls and 111 online reports. Analyses are broken down by NHS region. We also look for estimates of recent growth rate and associated doubling / halving time.
2.2 Reports by region over time
tab_date_region_all <- x %>%
filter(!is.na(nhs_region)) %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
dth %>%
mutate(trusted = case_when(date_report < max(dth$date_report)-delay_max ~ "Y",
date_report >= max(dth$date_report)-delay_max ~ "N"),
value = "Deaths",
vline = max(dth$date_report)-delay_max-1,
lab = "Truncated for reporting delay",
lab_pos_x = vline + 10,
lab_pos_y = 150,
lab_col = "darkgrey") %>%
rename(date = date_report,
n = deaths) %>%
bind_rows(
mutate(tab_date_region_all, value = "Reports",
trusted = "Y",
vline = as.Date("2020-03-23"),
lab = "Start of UK lockdown",
lab_pos_x = vline - 8,
lab_pos_y = 30200,
lab_col = "black")
) %>%
mutate(value = factor(value, levels = c("Reports","Deaths"))) -> dths_reports
plot_dth_report <-
ggplot(dths_reports, aes(date, n, colour = nhs_region)) +
# Add main points and lines, coloured by region and fade out deaths for excluded period
geom_point(aes(alpha = trusted)) +
geom_line(alpha = 0.2) +
geom_smooth(method = "loess", span = .5, color = "black") +
scale_colour_manual("", values = pal) +
scale_alpha_manual(values = c(0.3,1)) +
guides(alpha = F) +
# Add vertical markers for important dates with labels - different for each facet
ggnewscale::new_scale_colour() +
geom_vline(aes(xintercept = vline, col = value), lty = "solid") +
geom_text(aes(x = lab_pos_x, y = lab_pos_y, label = lab, col = value), size = 3) +
scale_colour_manual("",values = c("black","darkgrey"), guide = F) +
# Facet by deaths and reports
facet_grid(rows = vars(value), scales = "free_y", switch = "y") +
# Other formatting
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",strip.placement = "outside") +
rotate_x +
labs(x = NULL,
y = NULL)
plot_dth_report
2.3 Reports by region by age over time
We plot the number of 111/999 calls and 111 online reports by age, and the proportion of 111/999 calls and 111 online reports by age. In the second graph, the vertical lines indicate the proportion of individuals residing in the corresponding NHS region who belong to the corresponding age group.
tab_date_region_age_all <- x %>%
filter(!is.na(nhs_region),
age != "missing") %>%
group_by(date, nhs_region, age) %>%
summarise(n = sum(count))
tab_date_region_age_all %>%
ggplot(aes(x = date, y = n, fill = age)) +
geom_col(position = "stack") +
scale_fill_manual(values = age.pal) +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
axis.text.x = element_text(angle = 90, hjust = 1)) +
guides(fill = guide_legend(title = "Age", ncol = 3)) +
labs(x = NULL,
y = "Total daily reports by age") +
facet_wrap(~ nhs_region, ncol = 4)
tab_date_region_age_all <- tab_date_region_age_all %>%
group_by(date, nhs_region) %>%
summarise(tot = sum(n)) %>%
left_join(tab_date_region_age_all, by = c("date", "nhs_region")) %>%
mutate(prop_n = n/tot)
tab_date_region_age_all %>%
ggplot(aes(x = date, y = prop_n, color = age)) +
scale_color_manual(values = age.pal) +
geom_line() +
geom_point() +
geom_hline(data = nhs_region_pop, aes(yintercept = value, color = variable)) +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
axis.text.x = element_text(angle = 90, hjust = 1)) +
guides(color = guide_legend(title = "Age", ncol = 3)) +
labs(x = NULL,
y = "Proportion of daily reports by age") +
facet_wrap(~ nhs_region, ncol = 4)
2.4 Moving window model
We fit quasi-Poisson GLMs for 14-day windows to get growth rates over time.
## set moving time window (1/2/3 weeks)
w <- 14
# create empty df
r_all_sliding <- NULL
## make data for model
x_model_all_moving <- x %>%
filter(!is.na(nhs_region)) %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
unique_dates <- unique(x_model_all_moving$date)
for (i in 1:(length(unique_dates) - w)) {
date_i <- unique_dates[i]
date_i_max <- date_i + w
model_data <- x_model_all_moving %>%
filter(date >= date_i & date < date_i_max) %>%
mutate(day = as.integer(date - date_i)) %>%
day_of_week()
mod <- glm(n ~ day * nhs_region + day_of_week,
data = model_data,
family = 'quasipoisson')
# get growth rate
r <- get_r(mod)
r$w_min <- date_i
r$w_max <- date_i_max
# combine all estimates
r_all_sliding <- bind_rows(r_all_sliding, r)
}
#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale,
w = 0.5)
#convert growth rates r to R0
r_all_sliding <- r_all_sliding %>%
mutate(R = epitrix::r2R0(r, SI_distribution),
R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))We examine the evolution of the growth rate by region over time.
# plot
plot_growth <-
r_all_sliding %>%
ggplot(aes(x = w_max, y = r)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 0, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(colour = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated daily growth rate (r)") +
scale_colour_manual(values = pal)From the growth rate, we derive R and examine its value through time.
# plot
plot_R <-
r_all_sliding %>%
ggplot(aes(x = w_max, y = R)) +
geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 1, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated effective reproduction\nnumber (Re)") +
scale_colour_manual(values = pal)
R <- r_all_sliding %>%
mutate(lower_95 = R_lower_95,
upper_95 = R_upper_95,
value = R,
measure = "R",
reference = 1)
r_R <- r_all_sliding %>%
mutate(measure = "r",
value = r,
reference = 0) %>%
bind_rows(R)
r_R %>%
ggplot(aes(x = w_max, y = value)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(aes(yintercept = reference), linetype = "dashed") +
theme_bw() +
scale_weeks +
rotate_x +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0,0, "cm"),
strip.background = element_blank(),
# strip.text.x = element_blank(),
strip.placement = "outside"
) +
guides(color = guide_legend(title = "",
override.aes = list(fill = NA)),
fill = FALSE) +
labs(x = "", y = "") +
scale_colour_manual(values = pal) +
facet_grid(rows = vars(measure),
scales = "free_y",
switch = "y",
labeller = as_labeller(c(r = "Daily growth rate (r)",
R = "Effective reproduction\nnumber (Re)")))
2.5 Moving window model - stratified by age
We repeat the above analysis, where we fit quasi-Poisson GLMs for 14-day windows to get growth rates over time, but apply this to each age group separately (0-18, 19-69, 70-120 years old).
We first run the analysis for 0-18 years old.
## set moving time window (2 weeks)
w <- 14
# create empty df
r_all_sliding_0_18 <- NULL
## make data for model
x_model_all_moving_0_18 <- x %>%
filter(!is.na(nhs_region),
age == "0-18") %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
unique_dates <- unique(x_model_all_moving_0_18$date)
for (i in 1:(length(unique_dates) - w)) {
date_i <- unique_dates[i]
date_i_max <- date_i + w
model_data <- x_model_all_moving_0_18 %>%
filter(date >= date_i & date < date_i_max) %>%
mutate(day = as.integer(date - date_i)) %>%
day_of_week()
mod <- glm(n ~ day * nhs_region + day_of_week,
data = model_data,
family = 'quasipoisson')
# get growth rate
r <- get_r(mod)
r$w_min <- date_i
r$w_max <- date_i_max
# combine all estimates
r_all_sliding_0_18 <- bind_rows(r_all_sliding_0_18, r)
}
#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale, w = 0.5)
#convert growth rates r to R0
r_all_sliding_0_18 <- r_all_sliding_0_18 %>%
mutate(R = epitrix::r2R0(r, SI_distribution),
R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))# plot
plot_growth <-
r_all_sliding_0_18 %>%
ggplot(aes(x = w_max, y = r)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 0, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated daily growth rate (r)"
) +
scale_colour_manual(values = pal)# plot
plot_R <-
r_all_sliding_0_18 %>%
ggplot(aes(x = w_max, y = R)) +
geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 1, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated effective reproduction\nnumber (Re)"
) +
scale_colour_manual(values = pal)
R <- r_all_sliding_0_18 %>%
mutate(lower_95 = R_lower_95,
upper_95 = R_upper_95,
value = R,
measure = "R",
reference = 1)
r_R <- r_all_sliding_0_18 %>%
mutate(measure = "r",
value = r,
reference = 0) %>%
bind_rows(R)
fig2_3_0_18 <- r_R %>%
ggplot(aes(x = w_max, y = value)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(aes(yintercept = reference), linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0,0, "cm"),
strip.background = element_blank(),
strip.placement = "outside"
) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "", y = "") +
scale_colour_manual(values = pal) +
facet_grid(rows = vars(measure),
scales = "free_y",
switch = "y",
labeller = as_labeller(c(r = "Daily growth rate (r)",
R = "Effective reproduction\nnumber (Re)")))Then, we run the analysis for 19-69 years old.
## set moving time window (2 weeks)
w <- 14
# create empty df
r_all_sliding_19_69 <- NULL
## make data for model
x_model_all_moving_19_69 <- x %>%
filter(!is.na(nhs_region),
age == "19-69") %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
unique_dates <- unique(x_model_all_moving_19_69$date)
for (i in 1:(length(unique_dates) - w)) {
date_i <- unique_dates[i]
date_i_max <- date_i + w
model_data <- x_model_all_moving_19_69 %>%
filter(date >= date_i & date < date_i_max) %>%
mutate(day = as.integer(date - date_i)) %>%
day_of_week()
mod <- glm(n ~ day * nhs_region + day_of_week,
data = model_data,
family = 'quasipoisson')
# get growth rate
r <- get_r(mod)
r$w_min <- date_i
r$w_max <- date_i_max
# combine all estimates
r_all_sliding_19_69 <- bind_rows(r_all_sliding_19_69, r)
}
#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale, w = 0.5)
#convert growth rates r to R0
r_all_sliding_19_69 <- r_all_sliding_19_69 %>%
mutate(R = epitrix::r2R0(r, SI_distribution),
R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))# plot
plot_growth <-
r_all_sliding_19_69 %>%
ggplot(aes(x = w_max, y = r)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 0, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(colour = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated daily growth rate (r)") +
scale_colour_manual(values = pal)# plot
plot_R <-
r_all_sliding_19_69 %>%
ggplot(aes(x = w_max, y = R)) +
geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 1, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated effective reproduction\nnumber (Re)"
) +
scale_colour_manual(values = pal)
R <- r_all_sliding_19_69 %>%
mutate(lower_95 = R_lower_95,
upper_95 = R_upper_95,
value = R,
measure = "R",
reference = 1)
r_R <- r_all_sliding_19_69 %>%
mutate(measure = "r",
value = r,
reference = 0) %>%
bind_rows(R)
fig2_3_19_69 <- r_R %>%
ggplot(aes(x = w_max, y = value)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(aes(yintercept = reference), linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0,0, "cm"),
strip.background = element_blank(),
strip.placement = "outside"
) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "", y = "") +
scale_colour_manual(values = pal) +
facet_grid(rows = vars(measure),
scales = "free_y",
switch = "y",
labeller = as_labeller(c(r = "Daily growth rate (r)",
R = "Effective reproduction\nnumber (Re)")))Finally, we run the analysis for 70-120 years old.
## set moving time window (2 weeks)
w <- 14
# create empty df
r_all_sliding_70_120 <- NULL
## make data for model
x_model_all_moving_70_120 <- x %>%
filter(!is.na(nhs_region),
age == "70-120") %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
unique_dates <- unique(x_model_all_moving_70_120$date)
for (i in 1:(length(unique_dates) - w)) {
date_i <- unique_dates[i]
date_i_max <- date_i + w
model_data <- x_model_all_moving_70_120 %>%
filter(date >= date_i & date < date_i_max) %>%
mutate(day = as.integer(date - date_i)) %>%
day_of_week()
mod <- glm(n ~ day * nhs_region + day_of_week,
data = model_data,
family = 'quasipoisson')
# get growth rate
r <- get_r(mod)
r$w_min <- date_i
r$w_max <- date_i_max
# combine all estimates
r_all_sliding_70_120 <- bind_rows(r_all_sliding_70_120, r)
}
#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale, w = 0.5)
#convert growth rates r to R0
r_all_sliding_70_120 <- r_all_sliding_70_120 %>%
mutate(R = epitrix::r2R0(r, SI_distribution),
R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))# plot
plot_growth <-
r_all_sliding_70_120 %>%
ggplot(aes(x = w_max, y = r)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 0, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated daily growth rate (r)"
) +
scale_colour_manual(values = pal)# plot
plot_R <-
r_all_sliding_70_120 %>%
ggplot(aes(x = w_max, y = R)) +
geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 1, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated effective reproduction\nnumber (Re)") +
scale_colour_manual(values = pal)
R <- r_all_sliding_70_120 %>%
mutate(lower_95 = R_lower_95,
upper_95 = R_upper_95,
value = R,
measure = "R",
reference = 1)
r_R <- r_all_sliding_70_120 %>%
mutate(measure = "r",
value = r,
reference = 0) %>%
bind_rows(R)
fig2_3_70_120 <- r_R %>%
ggplot(aes(x = w_max, y = value)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(aes(yintercept = reference), linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0,0, "cm"),
strip.background = element_blank(),
strip.placement = "outside"
) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "", y = "") +
scale_colour_manual(values = pal) +
facet_grid(rows = vars(measure),
scales = "free_y",
switch = "y",
labeller = as_labeller(c(r = "Daily growth rate (r)",
R = "Effective reproduction\nnumber (Re)"))) We combine the estimated growth rates and effective reproduction numbers into a single figure.
ggpubr::ggarrange(fig2_3_0_18,
fig2_3_19_69,
fig2_3_70_120,
nrow = 3,
labels = "AUTO",
common.legend = TRUE,
legend = "bottom",
align = "hv") 
3 Comparison with deaths time series
3.1 Outline
We want to explore the correlation between NHS Pathways reports and deaths, and assess the potential for reports to be used as an early warning system for disease resurgence.
Death data are publically available. We truncate the time series to avoid bias from reporting delay - we assume a conservative delay of three weeks.
3.2 Lagged correlation
We calculate Pearson’s correlation coefficient between deaths and NHS Pathways notifications using different lags. Confidence intervals are obtained using bootstrap. Note that results were also confirmed using Spearman’s rank correlation.
First we join the NHS Pathways and death data, and aggregate over all England:
## truncate death data for reporting delay
trunc_date <- max(dth$date_report) - delay_max
dth_trunc <- dth %>%
rename(date = date_report) %>%
filter(date <= trunc_date)
## join with notification data
all_data <- x %>%
filter(!is.na(nhs_region)) %>%
group_by(date, nhs_region) %>%
summarise(count = sum(count, na.rm = T)) %>%
ungroup %>%
inner_join(dth_trunc,
by = c("date","nhs_region"))
all_tot <- all_data %>%
group_by(date) %>%
summarise(count = sum(count, na.rm = TRUE),
deaths = sum(deaths, na.rm = TRUE)) We calculate correlation with lagged NHS Pathways reports from 0 to 30 days behind deaths:
## Calculate all correlations + bootstrap CIs
lag_cor <- data.frame()
for (i in 0:30) {
## lag reports
summary <- all_tot %>%
mutate(note_lag = lag(count, i)) %>%
## calculate rank correlation and bootstrap CI
getboot(.) %>%
mutate(lag = i)
lag_cor <- bind_rows(lag_cor, summary)
}
cor_vs_lag <- ggplot(lag_cor, aes(lag, r)) +
theme_bw() +
geom_ribbon(aes(ymin = r_low, ymax = r_hi), alpha = 0.2) +
geom_hline(yintercept = 0, lty = "longdash") +
geom_point() +
geom_line() +
labs(x = "Lag between NHS pathways and death data (days)",
y = "Pearson's correlation") +
large_txt
cor_vs_lag
This analysis suggests that the best lag is 23 days. We then compare and plot the number of deaths reported against the number of NHS Pathways reports lagged by 23 days.
all_tot <- all_tot %>%
rename(date_death = date) %>%
mutate(note_lag = lag(count, lag_cor$lag[l_opt]),
note_lag_c = (note_lag - mean(note_lag, na.rm = T)),
date_note = lag(date_death,16))
lag_mod <- glm(deaths ~ note_lag, data = all_tot, family = "quasipoisson")
summary(lag_mod)
##
## Call:
## glm(formula = deaths ~ note_lag, family = "quasipoisson", data = all_tot)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -9.6508 -2.6590 -0.3036 3.1029 5.1790
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 4.926e+00 5.292e-02 93.09 <2e-16 ***
## note_lag 1.181e-05 5.318e-07 22.20 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for quasipoisson family taken to be 11.55623)
##
## Null deviance: 6084.69 on 50 degrees of freedom
## Residual deviance: 583.33 on 49 degrees of freedom
## (23 observations deleted due to missingness)
## AIC: NA
##
## Number of Fisher Scoring iterations: 4
exp(coefficients(lag_mod))
## (Intercept) note_lag
## 137.816088 1.000012
exp(confint(lag_mod))
## 2.5 % 97.5 %
## (Intercept) 124.094583 152.703757
## note_lag 1.000011 1.000013
Rsq(lag_mod)
## [1] 0.9041319
mod_fit <- as.data.frame(predict(lag_mod, type = "link", se.fit = TRUE)[1:2])
all_tot_pred <-
all_tot %>%
filter(!is.na(note_lag)) %>%
mutate(pred = mod_fit$fit,
pred.se = mod_fit$se.fit,
low = exp(pred - 1.96*pred.se),
hi = exp(pred + 1.96*pred.se))
glm_fit <- all_tot_pred %>%
filter(!is.na(note_lag)) %>%
ggplot(aes(x = note_lag, y = deaths)) +
geom_point() +
geom_line(aes(y = exp(pred))) +
geom_ribbon(aes(ymin = low, ymax = hi), alpha = 0.3, col = "grey") +
theme_bw() +
labs(y = "Daily number of\ndeaths reported",
x = "Daily number of NHS Pathways reports") +
large_txt
glm_fit
4 Supplementary figures
4.1 Serial interval distribution
This is a comparison of gamma versus lognormal distribution for the serial interval used to convert r to R in our analysis. Both distributions are parameterised with mean 4.7 and standard deviation 2.9.
SI_param <- epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale, w = 0.5)
SI_distribution2 <- distcrete::distcrete("lnorm", interval = 1,
meanlog = log(4.7),
sdlog = log(2.9), w = 0.5)
SI_dist1 <- data.frame(x = SI_distribution$r(1e5))
SI_dist1 <- count(SI_dist1, x) %>%
ggplot() +
geom_col(aes(x = x, y = n)) +
labs(x = "Serial interval (days)", y = "Frequency") +
scale_x_continuous(breaks = seq(0, 30, 5)) +
theme_bw()
SI_dist2 <- data.frame(x = SI_distribution2$r(1e5))
SI_dist2 <- count(SI_dist2, x) %>%
ggplot() +
geom_col(aes(x = x, y = n)) +
labs(x = "Serial interval (days)", y = "Frequency") +
scale_x_continuous(breaks = seq(0, 200, 20), limits = c(0, 200)) +
theme_bw()
ggpubr::ggarrange(SI_dist1,
SI_dist2,
nrow = 1,
labels = "AUTO") 
4.2 Sensitivity analysis - 7 or 21 days moving window
We reproduce the window analysis with either a 7 or 21 days window for sensitivity purposes.
First with the 7 days window:
## set moving time window (1/2/3 weeks)
w <- 7
# create empty df
r_all_sliding_7days <- NULL
## make data for model
x_model_all_moving <- x %>%
filter(!is.na(nhs_region)) %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
unique_dates <- unique(x_model_all_moving$date)
for (i in 1:(length(unique_dates) - w)) {
date_i <- unique_dates[i]
date_i_max <- date_i + w
model_data <- x_model_all_moving %>%
filter(date >= date_i & date < date_i_max) %>%
mutate(day = as.integer(date - date_i)) %>%
day_of_week()
mod <- glm(n ~ day * nhs_region + day_of_week,
data = model_data,
family = 'quasipoisson')
# get growth rate
r <- get_r(mod)
r$w_min <- date_i
r$w_max <- date_i_max
# combine all estimates
r_all_sliding_7days <- bind_rows(r_all_sliding_7days, r)
}
#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale,
w = 0.5)
#convert growth rates r to R0
r_all_sliding_7days <- r_all_sliding_7days %>%
mutate(R = epitrix::r2R0(r, SI_distribution),
R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))# plot
plot_growth <-
r_all_sliding_7days %>%
ggplot(aes(x = w_max, y = r)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 0, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated daily growth rate (r)") +
scale_colour_manual(values = pal)plot_R <- r_all_sliding_7days %>%
ggplot(aes(x = w_max, y = R)) +
geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 1, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated effective reproduction\nnumber (Re)") +
scale_colour_manual(values = pal)
R <- r_all_sliding_7days %>%
mutate(lower_95 = R_lower_95,
upper_95 = R_upper_95,
value = R,
measure = "R",
reference = 1)
r_R <- r_all_sliding_7days %>%
mutate(measure = "r",
value = r,
reference = 0) %>%
bind_rows(R)
r_R_7 <- r_R %>%
ggplot(aes(x = w_max, y = value)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(aes(yintercept = reference), linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0,0, "cm"),
strip.background = element_blank(),
strip.placement = "outside"
) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "", y = "") +
scale_colour_manual(values = pal) +
facet_grid(rows = vars(measure),
scales = "free_y",
switch = "y",
labeller = as_labeller(c(r = "Daily growth rate (r)",
R = "Effective reproduction\nnumber (Re)")))Then with the 21 days window:
## set moving time window (1/2/3 weeks)
w <- 21
# create empty df
r_all_sliding_21days <- NULL
## make data for model
x_model_all_moving <- x %>%
filter(!is.na(nhs_region)) %>%
group_by(date, nhs_region) %>%
summarise(n = sum(count))
unique_dates <- unique(x_model_all_moving$date)
for (i in 1:(length(unique_dates) - w)) {
date_i <- unique_dates[i]
date_i_max <- date_i + w
model_data <- x_model_all_moving %>%
filter(date >= date_i & date < date_i_max) %>%
mutate(day = as.integer(date - date_i)) %>%
day_of_week()
mod <- glm(n ~ day * nhs_region + day_of_week,
data = model_data,
family = 'quasipoisson')
# get growth rate
r <- get_r(mod)
r$w_min <- date_i
r$w_max <- date_i_max
# combine all estimates
r_all_sliding_21days <- bind_rows(r_all_sliding_21days, r)
}
#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
shape = SI_param$shape,
scale = SI_param$scale,
w = 0.5)
#convert growth rates r to R0
r_all_sliding_21days <- r_all_sliding_21days %>%
mutate(R = epitrix::r2R0(r, SI_distribution),
R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))# plot
plot_growth <-
r_all_sliding_21days %>%
ggplot(aes(x = w_max, y = r)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 0, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated daily growth rate (r)") +
scale_colour_manual(values = pal)# plot
plot_R <-
r_all_sliding_21days %>%
ggplot(aes(x = w_max, y = R)) +
geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(yintercept = 1, linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "",
y = "Estimated effective reproduction\nnumber (Re)") +
scale_colour_manual(values = pal)
R <- r_all_sliding_21days %>%
mutate(lower_95 = R_lower_95,
upper_95 = R_upper_95,
value = R,
measure = "R",
reference = 1)
r_R <- r_all_sliding_21days %>%
mutate(measure = "r",
value = r,
reference = 0) %>%
bind_rows(R)
r_R_21 <- r_R %>%
ggplot(aes(x = w_max, y = value)) +
geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
geom_line(aes(colour = nhs_region)) +
geom_point(aes(colour = nhs_region)) +
geom_hline(aes(yintercept = reference), linetype = "dashed") +
theme_bw() +
scale_weeks +
theme(legend.position = "bottom",
plot.margin = margin(0.5,1,0,0, "cm"),
strip.background = element_blank(),
strip.placement = "outside"
) +
guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
labs(x = "", y = "") +
scale_colour_manual(values = pal) +
facet_grid(rows = vars(measure),
scales = "free_y",
switch = "y",
labeller = as_labeller(c(r = "Daily growth rate (r)",
R = "Effective reproduction\nnumber (Re)")))And we combine both outputs into a single plot:
ggpubr::ggarrange(r_R_7,
r_R_21,
nrow = 2,
labels = "AUTO",
common.legend = TRUE,
legend = "bottom") 
4.3 Correlation between NHS Pathways reports and deaths by NHS region
lag_cor_reg <- data.frame()
for (i in 0:30) {
summary <-
all_data %>%
group_by(nhs_region) %>%
mutate(note_lag = lag(count, i)) %>%
## calculate rank correlation and bootstrap CI for each region
group_modify(~getboot(.x)) %>%
mutate(lag = i)
lag_cor_reg <- bind_rows(lag_cor_reg, summary)
}
cor_vs_lag_reg <-
lag_cor_reg %>%
ggplot(aes(lag, r, col = nhs_region)) +
geom_hline(yintercept = 0, lty = "longdash") +
geom_ribbon(aes(ymin = r_low, ymax = r_hi, col = NULL, fill = nhs_region), alpha = 0.2) +
geom_point() +
geom_line() +
facet_wrap(~nhs_region) +
scale_color_manual(values = pal) +
scale_fill_manual(values = pal, guide = F) +
theme_bw() +
labs(x = "Lag between NHS pathways and death data (days)", y = "Pearson's correlation", col = "NHS region") +
theme(legend.position = "bottom") +
guides(color = guide_legend(override.aes = list(fill = NA)))
cor_vs_lag_reg
5 Export data
We save the tables created during our analysis:
if (!dir.exists("excel_tables")) {
dir.create("excel_tables")
}
## list all tables, and loop over export
tables_to_export <- c("r_all_sliding", "lag_cor")
for (e in tables_to_export) {
rio::export(get(e),
file.path("excel_tables",
paste0(e, ".xlsx")))
}
## also export result from regression on lagged data
rio::export(lag_mod, file.path("excel_tables", "lag_mod.rds"))6 System information
6.1 Outline
The following information documents the system on which the document was compiled.
6.2 System
This provides information on the operating system.
6.3 R environment
This provides information on the version of R used:
6.4 R packages
This provides information on the packages used:
sessionInfo()
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Catalina 10.15.5
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggnewscale_0.4.1 ggpubr_0.3.0 lubridate_1.7.9
## [4] chngpt_2020.5-21 cyphr_1.1.0 DT_0.13
## [7] kableExtra_1.1.0 janitor_2.0.1 remotes_2.1.1
## [10] projections_0.4.1 earlyR_0.0.1 epitrix_0.2.2
## [13] distcrete_1.0.3 incidence_1.7.1 rio_0.5.16
## [16] reshape2_1.4.4 rvest_0.3.5 xml2_1.3.2
## [19] linelist_0.0.40.9000 forcats_0.5.0 stringr_1.4.0
## [22] dplyr_1.0.0 purrr_0.3.4 readr_1.3.1
## [25] tidyr_1.1.0 tibble_3.0.1 ggplot2_3.3.2
## [28] tidyverse_1.3.0 here_0.1 reportfactory_0.0.5
##
## loaded via a namespace (and not attached):
## [1] colorspace_1.4-1 selectr_0.4-2 ggsignif_0.6.0 ellipsis_0.3.1
## [5] rprojroot_1.3-2 snakecase_0.11.0 fs_1.4.1 rstudioapi_0.11
## [9] farver_2.0.3 fansi_0.4.1 splines_3.6.3 knitr_1.28
## [13] jsonlite_1.6.1 broom_0.5.6 dbplyr_1.4.4 compiler_3.6.3
## [17] httr_1.4.1 backports_1.1.8 assertthat_0.2.1 Matrix_1.2-18
## [21] cli_2.0.2 htmltools_0.5.0 prettyunits_1.1.1 tools_3.6.3
## [25] gtable_0.3.0 glue_1.4.1 Rcpp_1.0.4.6 carData_3.0-4
## [29] cellranger_1.1.0 vctrs_0.3.1 nlme_3.1-144 matchmaker_0.1.1
## [33] crosstalk_1.1.0.1 xfun_0.15 ps_1.3.3 openxlsx_4.1.5
## [37] lifecycle_0.2.0 rstatix_0.6.0 MASS_7.3-51.5 scales_1.1.1
## [41] hms_0.5.3 sodium_1.1 yaml_2.2.1 curl_4.3
## [45] gridExtra_2.3 stringi_1.4.6 kyotil_2019.11-22 boot_1.3-24
## [49] pkgbuild_1.0.8 zip_2.0.4 rlang_0.4.6 pkgconfig_2.0.3
## [53] evaluate_0.14 lattice_0.20-38 labeling_0.3 htmlwidgets_1.5.1
## [57] cowplot_1.0.0 processx_3.4.2 tidyselect_1.1.0 plyr_1.8.6
## [61] magrittr_1.5 R6_2.4.1 generics_0.0.2 DBI_1.1.0
## [65] pillar_1.4.4 haven_2.3.1 foreign_0.8-75 withr_2.2.0
## [69] mgcv_1.8-31 survival_3.1-8 abind_1.4-5 modelr_0.1.8
## [73] crayon_1.3.4 car_3.0-8 utf8_1.1.4 rmarkdown_2.3
## [77] viridis_0.5.1 grid_3.6.3 readxl_1.3.1 data.table_1.12.8
## [81] blob_1.2.1 callr_3.4.3 reprex_0.3.0 digest_0.6.25
## [85] webshot_0.5.2 munsell_0.5.0 viridisLite_0.3.0